Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 162 of 182
Found at i:49368353 original size:3 final size:3
Alignment explanation
Indices: 49368347--49368372 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
49368337 TTTTTTATCT
49368347 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
49368373 TCATAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:49373576 original size:20 final size:20
Alignment explanation
Indices: 49373490--49373576 Score: 79
Period size: 20 Copynumber: 4.3 Consensus size: 20
49373480 CTTTTGGTAC
* *
49373490 TTTTTTTATTATTTTGGTTG
1 TTTTTTTACTGTTTTGGTTG
* *
49373510 CTATTTTTTGCTGTTTTTG-TG
1 -T-TTTTTTACTGTTTTGGTTG
* *
49373531 -TTTTTTACTGTTTTGATTT
1 TTTTTTTACTGTTTTGGTTG
49373550 TTTTTTTACTGTTTTGGTTG
1 TTTTTTTACTGTTTTGGTTG
49373570 TTATTTT
1 TT-TTTT
49373577 CATATTGTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
18 13 0.25
19 1 0.02
20 19 0.37
21 7 0.13
22 12 0.23
ACGTcount: A:0.08, C:0.05, G:0.15, T:0.72
Consensus pattern (20 bp):
TTTTTTTACTGTTTTGGTTG
Found at i:49373597 original size:35 final size:32
Alignment explanation
Indices: 49373541--49373643 Score: 93
Period size: 35 Copynumber: 3.2 Consensus size: 32
49373531 TTTTTTACTG
* * *
49373541 TTTTGATT-TTTTTTTTACTGTTTTGGTTGTTA
1 TTTTTATTGTTTTTATTGCTGTTTT-GTTGTTA
*
49373573 TTTTCATATTGTTTTTATTGCTGTTTTTGTTGCTA
1 TTTT--TATTGTTTTTATTGCTG-TTTTGTTGTTA
* * *
49373608 TTTTTGTTGTTTTTAATGTTG-TTTGTTGTTA
1 TTTTTATTGTTTTTATTGCTGTTTTGTTGTTA
49373639 TTTTT
1 TTTTT
49373644 GCTGCTGTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
31 14 0.24
32 4 0.07
33 14 0.24
34 3 0.05
35 20 0.34
36 4 0.07
ACGTcount: A:0.10, C:0.04, G:0.16, T:0.71
Consensus pattern (32 bp):
TTTTTATTGTTTTTATTGCTGTTTTGTTGTTA
Found at i:49373613 original size:12 final size:12
Alignment explanation
Indices: 49373584--49373671 Score: 60
Period size: 12 Copynumber: 7.8 Consensus size: 12
49373574 TTTCATATTG
* *
49373584 TTTTTATTGCTG
1 TTTTTGTTGCTA
49373596 TTTTTGTTGCTA
1 TTTTTGTTGCTA
49373608 TTTTTGTTG---
1 TTTTTGTTGCTA
**
49373617 TTTTTAATG-T-
1 TTTTTGTTGCTA
* *
49373627 TGTTTGTTGTTA
1 TTTTTGTTGCTA
* *
49373639 TTTTTGCTGCTG
1 TTTTTGTTGCTA
*
49373651 TTTTTGTTGTTA
1 TTTTTGTTGCTA
49373663 TTTTTGTTG
1 TTTTTGTTG
49373672 TTTGAATGTT
Statistics
Matches: 59, Mismatches: 14, Indels: 6
0.75 0.18 0.08
Matches are distributed among these distances:
9 7 0.12
10 6 0.10
11 1 0.02
12 45 0.76
ACGTcount: A:0.07, C:0.05, G:0.19, T:0.69
Consensus pattern (12 bp):
TTTTTGTTGCTA
Found at i:49373655 original size:43 final size:44
Alignment explanation
Indices: 49373596--49373687 Score: 125
Period size: 43 Copynumber: 2.1 Consensus size: 44
49373586 TTTATTGCTG
* *
49373596 TTTTTGTTGCTATTTTTGTTGTT-TTTAATGTTGTTTG-TTGTTA
1 TTTTTGCTGCTATTTTTGTTGTTATTT-ATGTTGTTTGAATGTTA
* *
49373639 TTTTTGCTGCTGTTTTTGTTGTTATTTTTGTTGTTTGAATGTTA
1 TTTTTGCTGCTATTTTTGTTGTTATTTATGTTGTTTGAATGTTA
49373683 TTTTT
1 TTTTT
49373688 TTATGCGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
43 30 0.70
44 13 0.30
ACGTcount: A:0.09, C:0.03, G:0.18, T:0.70
Consensus pattern (44 bp):
TTTTTGCTGCTATTTTTGTTGTTATTTATGTTGTTTGAATGTTA
Found at i:49373659 original size:31 final size:30
Alignment explanation
Indices: 49373594--49373661 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 30
49373584 TTTTTATTGC
*
49373594 TGTT-TTTGTTGCTATTTTTGTTGTTTTTAA
1 TGTTGTTTGTTGCTATTTTTGCTGTTTTT-A
*
49373624 TGTTGTTTGTTGTTATTTTTGCTGCTGTTTT-
1 TGTTGTTTGTTGCTATTTTTGCTG-T-TTTTA
49373655 TGTTGTT
1 TGTTGTT
49373662 ATTTTTGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 4 0.12
31 24 0.73
32 1 0.03
33 4 0.12
ACGTcount: A:0.06, C:0.04, G:0.21, T:0.69
Consensus pattern (30 bp):
TGTTGTTTGTTGCTATTTTTGCTGTTTTTA
Found at i:49373672 original size:12 final size:12
Alignment explanation
Indices: 49373629--49373673 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
49373619 TTTAATGTTG
49373629 TTTGTTGTTATT
1 TTTGTTGTTATT
* * *
49373641 TTTGCTGCTGTT
1 TTTGTTGTTATT
49373653 TTTGTTGTTATT
1 TTTGTTGTTATT
49373665 TTTGTTGTT
1 TTTGTTGTT
49373674 TGAATGTTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.04, C:0.04, G:0.20, T:0.71
Consensus pattern (12 bp):
TTTGTTGTTATT
Found at i:49373889 original size:38 final size:38
Alignment explanation
Indices: 49373800--49373887 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 38
49373790 TATCTTAATA
* * *
49373800 TAAT-TTTTTTTAATGTATTTTAAATTTATTTATTTTT
1 TAATATTTTTTTAATGTATTTTAAATGTATTTATATAT
*
49373837 TAATATTTGTTTTAATGT-TTTTAAGTGTATTTGATATAT
1 TAATATTT-TTTTAATGTATTTTAAATGTATTT-ATATAT
49373876 TATATATTTTTT
1 TA-ATATTTTTT
49373888 AAATTTGTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
37 4 0.09
38 15 0.35
39 18 0.42
40 6 0.14
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (38 bp):
TAATATTTTTTTAATGTATTTTAAATGTATTTATATAT
Found at i:49374531 original size:25 final size:25
Alignment explanation
Indices: 49374497--49374549 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
49374487 ATAAAAAAAT
*
49374497 TTATATAACATTTATATGCAGACGA
1 TTATATAACATTTATATCCAGACGA
49374522 TTATATAACATTTATATCCAGACGA
1 TTATATAACATTTATATCCAGACGA
49374547 TTA
1 TTA
49374550 CAAAGGCACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (25 bp):
TTATATAACATTTATATCCAGACGA
Found at i:49379883 original size:57 final size:58
Alignment explanation
Indices: 49379821--49379933 Score: 142
Period size: 57 Copynumber: 2.0 Consensus size: 58
49379811 CCCAATTATG
** *
49379821 ATTTTTTTTGTCACTTAATTATGATAAA-TTATAAAATAATCA-TTCAACTA-TCAGTAA
1 ATTTTTTTAATCACTTAATTATGA-AAAGTTACAAAATAATCACTT-AACTATTCAGTAA
* *
49379878 ATTTTTTTAATTATTTAATTATGAAAAGTTACAAAATAATCACTTAACTATTCAGT
1 ATTTTTTTAATCACTTAATTATGAAAAGTTACAAAATAATCACTTAACTATTCAGT
49379934 TTTGTCTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
56 3 0.06
57 38 0.79
58 7 0.15
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (58 bp):
ATTTTTTTAATCACTTAATTATGAAAAGTTACAAAATAATCACTTAACTATTCAGTAA
Found at i:49388731 original size:22 final size:22
Alignment explanation
Indices: 49388681--49388732 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 22
49388671 TCAAATATTC
*
49388681 ATATTTTATATTATAAAATATGA
1 ATATTTTATAATATAAAATA-GA
49388704 ATATTTTAATAATATAAAATA-A
1 ATATTTT-ATAATATAAAATAGA
49388726 ATATTTT
1 ATATTTT
49388733 TTTTTGTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 8 0.30
23 7 0.26
24 12 0.44
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATATTTTATAATATAAAATAGA
Found at i:49402289 original size:20 final size:20
Alignment explanation
Indices: 49402239--49402300 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
49402229 ATCAAGACTT
* * *
49402239 ATATATTATTATATAATTTAT
1 ATATATTA-TATAAAAATTAA
49402260 AT-TATATATATAAAAATTAA
1 ATATAT-TATATAAAAATTAA
* *
49402280 ATATATTATATTATAATTAA
1 ATATATTATATAAAAATTAA
49402300 A
1 A
49402301 AGTTTGTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
20 27 0.79
21 7 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATATTATATAAAAATTAA
Found at i:49405090 original size:13 final size:13
Alignment explanation
Indices: 49405072--49405096 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49405062 TTTCCAGCTG
49405072 TAAAATTTTTATT
1 TAAAATTTTTATT
49405085 TAAAATTTTTAT
1 TAAAATTTTTAT
49405097 ATGACTATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAAATTTTTATT
Found at i:49405550 original size:43 final size:42
Alignment explanation
Indices: 49405440--49405708 Score: 268
Period size: 43 Copynumber: 6.3 Consensus size: 42
49405430 TTATGAGGAA
* * *
49405440 AAACGTCGCTATAGAACATGGTCTTTAGCGGCGCTTTTCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAACGGCGCTTTTCCAC
* ** * * * *
49405482 AAATGCTACTACAGACCATGATCTTTAACGGCGCTTATTTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAACGGCGCTT-TTCCAC
*
49405525 AAACGCCGCTAAAGAACATGGTCTTTAATGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAACGGCGCTTTT-CCAC
* * * * *
49405568 AAACGCTGCTAAAGAACATGGTCTTTAACAGTGCTTATCCCAT
1 AAACGCCGCTAAAGAACATGGTCTTTAACGGCGCTT-TTCCAC
* * * *
49405611 AAACGCCGCTAAAGAACATGGTTTTTAGCAGCGCTTTTCTCGC
1 AAACGCCGCTAAAGAACATGGTCTTTAACGGCGCTTTTC-CAC
* * **
49405654 AAACGTCGCTAAAGAACATGGTCTTTAGCGGCATTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAACGGCGCTTTT-CCAC
*
49405697 AAACGCCACTAA
1 AAACGCCGCTAA
49405709 CATTAACAAA
Statistics
Matches: 184, Mismatches: 38, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
42 32 0.17
43 150 0.82
44 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGGTCTTTAACGGCGCTTTTCCAC
Found at i:49405620 original size:86 final size:86
Alignment explanation
Indices: 49405440--49405708 Score: 299
Period size: 86 Copynumber: 3.1 Consensus size: 86
49405430 TTATGAGGAA
* * * * * * *
49405440 AAACGTCGCTATAGAACATGGTCTTTAGCGGCGCTTTT-CCACAAATGCTACTACAGACCATGAT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCTGCTAAAGAACATGGT
* **
49405504 CTTTAACGGCGCTTATTTCAC
66 CTTTAACAGCGCTTATCCCAC
**
49405525 AAACGCCGCTAAAGAACATGGTCTTTAATGGCGCTTTTCCCACAAACGCTGCTAAAGAACATGGT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCTGCTAAAGAACATGGT
* *
49405590 CTTTAACAGTGCTTATCCCAT
66 CTTTAACAGCGCTTATCCCAC
* * * *
49405611 AAACGCCGCTAAAGAACATGGTTTTTAGCAGCGCTTTTCTCGCAAACG-TCGCTAAAGAACATGG
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCT-GCTAAAGAACATGG
* * ** *
49405675 TCTTTAGCGGCATTTTTCCCAC
65 TCTTTAACAGCGCTTATCCCAC
*
49405697 AAACGCCACTAA
1 AAACGCCGCTAA
49405709 CATTAACAAA
Statistics
Matches: 154, Mismatches: 28, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
85 35 0.23
86 119 0.77
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (86 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCACAAACGCTGCTAAAGAACATGGT
CTTTAACAGCGCTTATCCCAC
Found at i:49407701 original size:20 final size:21
Alignment explanation
Indices: 49407661--49407701 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
49407651 AATTTTTAGT
*
49407661 ATCAAAATTTAAAGGCAAAAC
1 ATCAAAATTTAAAGCCAAAAC
*
49407682 ATCAAAATTT-AATCCAAAAC
1 ATCAAAATTTAAAGCCAAAAC
49407702 GAGCCTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.56, C:0.17, G:0.05, T:0.22
Consensus pattern (21 bp):
ATCAAAATTTAAAGCCAAAAC
Found at i:49407740 original size:21 final size:21
Alignment explanation
Indices: 49407707--49407753 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
49407697 AAAACGAGCC
*
49407707 TTTTTTGCCTTTAAATTTTGAT
1 TTTTTTGCCTTTAAA-TTTGAA
*
49407729 TTTTTTG-GTTTAAATTTGAA
1 TTTTTTGCCTTTAAATTTGAA
49407749 TTTTT
1 TTTTT
49407754 AAATATTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.43
21 6 0.26
22 7 0.30
ACGTcount: A:0.19, C:0.04, G:0.11, T:0.66
Consensus pattern (21 bp):
TTTTTTGCCTTTAAATTTGAA
Found at i:49408172 original size:41 final size:40
Alignment explanation
Indices: 49408126--49408282 Score: 136
Period size: 41 Copynumber: 3.8 Consensus size: 40
49408116 GCGCTTTTTC
49408126 AAGCGTGACTAATGCTCTGACCTTTAACGACGCTTGTCCAT
1 AAGCGTG-CTAATGCTCTGACCTTTAACGACGCTTGTCCAT
* * * *
49408167 AAGCGTCGCTATTACTCTGACCTTTAACGGCACTT-TCACAT
1 AAGCGT-GCTAATGCTCTGACCTTTAACGACGCTTGTC-CAT
** * * *
49408208 AAGCGTGGCTAATGCTCTGAATTTTAGCGGCGCTTGCCCAT
1 AAGCGT-GCTAATGCTCTGACCTTTAACGACGCTTGTCCAT
* * * * *
49408249 AAGTGCCGTTATTGCTCTGACCTTTAGCGACGCT
1 AAGCG-TGCTAATGCTCTGACCTTTAACGACGCT
49408283 ATTGCTCTGA
Statistics
Matches: 93, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
40 2 0.02
41 89 0.96
42 2 0.02
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.31
Consensus pattern (40 bp):
AAGCGTGCTAATGCTCTGACCTTTAACGACGCTTGTCCAT
Found at i:49408290 original size:24 final size:24
Alignment explanation
Indices: 49408258--49408306 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
49408248 TAAGTGCCGT
49408258 TATTGCTCTGACCTTTAGCGACGC
1 TATTGCTCTGACCTTTAGCGACGC
*
49408282 TATTGCTCTGACCTTTAGCGGCGC
1 TATTGCTCTGACCTTTAGCGACGC
49408306 T
1 T
49408307 TTCCCATAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.14, C:0.29, G:0.22, T:0.35
Consensus pattern (24 bp):
TATTGCTCTGACCTTTAGCGACGC
Found at i:49408327 original size:65 final size:64
Alignment explanation
Indices: 49408215--49408337 Score: 174
Period size: 65 Copynumber: 1.9 Consensus size: 64
49408205 CATAAGCGTG
* * * *
49408215 GCTAATGCTCTGAATTTTAGCGGCGCTTGCCCATAAGTGCCGTTATTGCTCTGACCTTTAGCGAC
1 GCTAATGCTCTGAACTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTAT-ACCTTTAGCGAC
* * *
49408280 GCTATTGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCTATACCTTT
1 GCTAATGCTCTGAACTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTATACCTTT
49408338 TGCGGCGTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
64 6 0.12
65 45 0.88
ACGTcount: A:0.17, C:0.28, G:0.21, T:0.33
Consensus pattern (64 bp):
GCTAATGCTCTGAACTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTATACCTTTAGCGAC
Found at i:49408343 original size:40 final size:39
Alignment explanation
Indices: 49408274--49408387 Score: 111
Period size: 40 Copynumber: 2.8 Consensus size: 39
49408264 TCTGACCTTT
* * * *
49408274 AGCGACGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCATA
1 AGCGCCGCTATTGCTAT-ACCTTTTGCGGCG-TTTCCCAAA
***
49408315 AGCGCCGCTATTGCTATACCTTTTGCGGCGTTTATGTAAA
1 AGCGCCGCTATTGCTATACCTTTTGCGGCGTTT-CCCAAA
* * *
49408355 AACACCGCTATTGCTTTACCTTTTGCGGCGTTT
1 AGCGCCGCTATTGCTATACCTTTTGCGGCGTTT
49408388 TCCGTCCAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
39 3 0.05
40 44 0.71
41 15 0.24
ACGTcount: A:0.18, C:0.27, G:0.21, T:0.34
Consensus pattern (39 bp):
AGCGCCGCTATTGCTATACCTTTTGCGGCGTTTCCCAAA
Found at i:49414009 original size:38 final size:38
Alignment explanation
Indices: 49413958--49414032 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
49413948 TCACTATATA
*
49413958 TTTTTAAATTAAAAA-ATATATTAAATATAAAAATGTGAT
1 TTTTTAAATTAAAAATA-ATATTAAAAAT-AAAATGTGAT
* *
49413997 TTTTTTAA-TAAAAATAATTTTAAAAATAAAATGTGA
1 TTTTTAAATTAAAAATAATATTAAAAATAAAATGTGA
49414033 AATTGATACC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 9 0.28
38 15 0.47
39 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.41
Consensus pattern (38 bp):
TTTTTAAATTAAAAATAATATTAAAAATAAAATGTGAT
Found at i:49415730 original size:23 final size:23
Alignment explanation
Indices: 49415684--49415731 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
49415674 GGTGAAAGAT
* * *
49415684 AATATCTAATAATATTCTATTAA
1 AATATCTAATAATAATATACTAA
*
49415707 AATATCTAATAATAATATCCTAA
1 AATATCTAATAATAATATACTAA
49415730 AA
1 AA
49415732 CTATTATTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (23 bp):
AATATCTAATAATAATATACTAA
Found at i:49426257 original size:23 final size:23
Alignment explanation
Indices: 49426231--49426306 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
49426221 AGTGCTGGGT
49426231 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* * *
49426254 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACACAGTGCTA
* *
49426277 ATCAGAGAGCACGAGAC-GTGCTA
1 AACAGAGAGCAC-ACACAGTGCTA
*
49426300 AATAGAG
1 AACAGAG
49426307 CGCGCGCTAG
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
23 40 0.95
24 2 0.05
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:49429895 original size:18 final size:18
Alignment explanation
Indices: 49429872--49429918 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
49429862 TGTTTTTAAC
*
49429872 TAATATATTAATTAATAA
1 TAATATATTAATAAATAA
49429890 TAATAT-TATAATAAATAA
1 TAATATAT-TAATAAATAA
49429908 TAATAATATTA
1 TAAT-ATATTA
49429919 TTTATATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 1 0.04
18 19 0.76
19 4 0.16
20 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATATATTAATAAATAA
Found at i:49429908 original size:21 final size:21
Alignment explanation
Indices: 49429875--49429919 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
49429865 TTTTAACTAA
* *
49429875 TATATTAATTAATAATAATAT
1 TATAATAAATAATAATAATAT
49429896 TATAATAAATAATAATAATAT
1 TATAATAAATAATAATAATAT
49429917 TAT
1 TAT
49429920 TTATATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TATAATAAATAATAATAATAT
Found at i:49433828 original size:20 final size:19
Alignment explanation
Indices: 49433790--49433828 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
49433780 AACAAAGTTT
*
49433790 AATAAAAACCTAAAATTAA
1 AATAAAAAACTAAAATTAA
*
49433809 AATAAAATAACTACAATTAA
1 AATAAAA-AACTAAAATTAA
49433829 GCCTCTGTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (19 bp):
AATAAAAAACTAAAATTAA
Found at i:49436857 original size:20 final size:19
Alignment explanation
Indices: 49436821--49436861 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
49436811 AAATTTTAAA
49436821 ATTAAAAAAAATATAAAAT
1 ATTAAAAAAAATATAAAAT
49436840 ATTAAAAAATTAAT-TAAAAT
1 ATTAAAAAA--AATATAAAAT
49436860 AT
1 AT
49436862 AGAGATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.45
20 8 0.40
21 3 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATTAAAAAAAATATAAAAT
Found at i:49437473 original size:20 final size:20
Alignment explanation
Indices: 49437448--49437488 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
49437438 AAAAACACAT
* *
49437448 AAAAATAACATTCAAACAAC
1 AAAAATAACAGTAAAACAAC
49437468 AAAAATAACAGTAAAACAAC
1 AAAAATAACAGTAAAACAAC
49437488 A
1 A
49437489 TTAAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.68, C:0.17, G:0.02, T:0.12
Consensus pattern (20 bp):
AAAAATAACAGTAAAACAAC
Found at i:49437483 original size:32 final size:33
Alignment explanation
Indices: 49437441--49437518 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 33
49437431 CAATAGTAAA
*
49437441 AACACATAAAAATAACATT-CAAACAACAAAAAT
1 AACA-ATAAAAATAACATTAAAAACAACAAAAAT
* * *
49437474 AACAGT-AAAACAACATTAAAAATAACAAAAAT
1 AACAATAAAAATAACATTAAAAACAACAAAAAT
*
49437506 AGCAATAAAAATA
1 AACAATAAAAATA
49437519 GCAACAACAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
31 10 0.28
32 17 0.47
33 9 0.25
ACGTcount: A:0.68, C:0.14, G:0.03, T:0.15
Consensus pattern (33 bp):
AACAATAAAAATAACATTAAAAACAACAAAAAT
Found at i:49437530 original size:12 final size:12
Alignment explanation
Indices: 49437497--49437563 Score: 55
Period size: 12 Copynumber: 5.6 Consensus size: 12
49437487 CATTAAAAAT
49437497 AACAAAAATAGC
1 AACAAAAATAGC
*
49437509 AATAAAAATAGC
1 AACAAAAATAGC
* *
49437521 AACAACAATAAC
1 AACAAAAATAGC
* * *
49437533 AGCAAAAAGAAC
1 AACAAAAATAGC
*
49437545 -ACGAAAATAGC
1 AACAAAAATAGC
49437556 AATCAAAA
1 AA-CAAAA
49437564 CAATAAAAAA
Statistics
Matches: 41, Mismatches: 12, Indels: 3
0.73 0.21 0.05
Matches are distributed among these distances:
11 7 0.17
12 30 0.73
13 4 0.10
ACGTcount: A:0.66, C:0.16, G:0.09, T:0.09
Consensus pattern (12 bp):
AACAAAAATAGC
Found at i:49437619 original size:19 final size:19
Alignment explanation
Indices: 49437559--49437628 Score: 81
Period size: 19 Copynumber: 3.6 Consensus size: 19
49437549 AAATAGCAAT
49437559 CAAAACAATAAAAAACAAC
1 CAAAACAATAAAAAACAAC
*
49437578 TCAAAA-AAAAAAAACATCAAC
1 -CAAAACAATAAAAA-A-CAAC
49437599 CAAAACAATAAAAAAGC-AC
1 CAAAACAATAAAAAA-CAAC
49437618 CAAAACAATAA
1 CAAAACAATAA
49437629 TATAATTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 20 0.45
20 13 0.30
21 11 0.25
ACGTcount: A:0.71, C:0.20, G:0.01, T:0.07
Consensus pattern (19 bp):
CAAAACAATAAAAAACAAC
Found at i:49438362 original size:14 final size:14
Alignment explanation
Indices: 49438343--49438387 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
49438333 TTGACATTGC
*
49438343 GAATAAAATAAGAA
1 GAATAAAAAAAGAA
49438357 GAATAAAAAAAGCAA
1 GAATAAAAAAAG-AA
*
49438372 -AAAAAAAAAAGAA
1 GAATAAAAAAAGAA
49438385 GAA
1 GAA
49438388 GAAAGAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 2 0.07
14 23 0.85
15 2 0.07
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (14 bp):
GAATAAAAAAAGAA
Found at i:49439560 original size:3 final size:3
Alignment explanation
Indices: 49439552--49439585 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
49439542 TTTATGTCGT
49439552 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
49439586 CTTTTTACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:49446469 original size:16 final size:15
Alignment explanation
Indices: 49446444--49446473 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
49446434 GTCACATTGT
49446444 AAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAC
49446459 AAAAAACAAAAAAAA
1 AAAAAA-AAAAAAAA
49446474 GGAATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAC
Found at i:49462154 original size:13 final size:13
Alignment explanation
Indices: 49462136--49462160 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49462126 GGTAATTGAC
49462136 TAATTGTTAATTA
1 TAATTGTTAATTA
49462149 TAATTGTTAATT
1 TAATTGTTAATT
49462161 CGATGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
TAATTGTTAATTA
Found at i:49462292 original size:143 final size:143
Alignment explanation
Indices: 49462034--49462325 Score: 550
Period size: 143 Copynumber: 2.0 Consensus size: 143
49462024 CTATTTTATG
* *
49462034 TTAACTTGTGTGCCATGTGCATTGGAGAAAAAAACTATTTCATGCAGTAGTGGAAAGGTGATTGG
1 TTAACTTGTGTGCCATGTGCATTGCAGAAAAAAACTATTTCATGCAGTAGGGGAAAGGTGATTGG
49462099 AACCACTTTATTAATATATATTTGTTTGGTAATTGACTAATTGTTAATTATAATTGTTAATTCGA
66 AACCACTTTATTAATATATATTTGTTTGGTAATTGACTAATTGTTAATTATAATTGTTAATTCGA
49462164 TGAATTGATTT-TA
131 TGAATTG-TTTGTA
49462177 TTAACTTGTGTGCCATGTGCATTGCAGAAAAAAACTATTTCATGCAGTAGGGGAAAGGTGATTGG
1 TTAACTTGTGTGCCATGTGCATTGCAGAAAAAAACTATTTCATGCAGTAGGGGAAAGGTGATTGG
49462242 AACCACTTTATTAATATATATTTGTTTGGTAATTGACTAATTGTTAATTATAATTGTTAATTCGA
66 AACCACTTTATTAATATATATTTGTTTGGTAATTGACTAATTGTTAATTATAATTGTTAATTCGA
49462307 TGAATTGTTTGTA
131 TGAATTGTTTGTA
49462320 TTAACT
1 TTAACT
49462326 GATTATTTAA
Statistics
Matches: 146, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
142 3 0.02
143 143 0.98
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (143 bp):
TTAACTTGTGTGCCATGTGCATTGCAGAAAAAAACTATTTCATGCAGTAGGGGAAAGGTGATTGG
AACCACTTTATTAATATATATTTGTTTGGTAATTGACTAATTGTTAATTATAATTGTTAATTCGA
TGAATTGTTTGTA
Found at i:49462315 original size:16 final size:13
Alignment explanation
Indices: 49462279--49462303 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49462269 GGTAATTGAC
49462279 TAATTGTTAATTA
1 TAATTGTTAATTA
49462292 TAATTGTTAATT
1 TAATTGTTAATT
49462304 CGATGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
TAATTGTTAATTA
Found at i:49465046 original size:17 final size:18
Alignment explanation
Indices: 49465024--49465083 Score: 88
Period size: 17 Copynumber: 3.3 Consensus size: 18
49465014 GTTTAAATTG
49465024 ATTT-AATTTATTTTTAA
1 ATTTAAATTTATTTTTAA
49465041 ATTTAAATTTA-TTTTAA
1 ATTTAAATTTATTTTTAA
49465058 ATTTAAATTTATCTTTTTAA
1 ATTTAAATTTA--TTTTTAA
49465078 ATTTAA
1 ATTTAA
49465084 TCAAATTTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
17 21 0.54
18 6 0.15
20 12 0.31
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTAAATTTATTTTTAA
Found at i:49465056 original size:23 final size:23
Alignment explanation
Indices: 49465024--49465068 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
49465014 GTTTAAATTG
**
49465024 ATTTAATTTATTTTTAAATTTAA
1 ATTTAATTTAAATTTAAATTTAA
*
49465047 ATTTATTTTAAATTTAAATTTA
1 ATTTAATTTAAATTTAAATTTA
49465069 TCTTTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTTAATTTAAATTTAAATTTAA
Found at i:49465083 original size:6 final size:6
Alignment explanation
Indices: 49465036--49465068 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
49465026 TTAATTTATT
*
49465036 TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
49465069 TCTTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:49466570 original size:30 final size:29
Alignment explanation
Indices: 49466535--49466711 Score: 156
Period size: 30 Copynumber: 6.0 Consensus size: 29
49466525 AGAAGCCCCT
* *
49466535 AAACTTTTTGAAAATTATATTTTGACTCCA
1 AAACTTTTTAAAAATTATATTTTAAC-CCA
* *
49466565 AAACTTTTTAAAAATTATATTTTGACCCCT
1 AAACTTTTTAAAAATTATATTTT-AACCCA
** *
49466595 AAACTTTTCCAAAATTATATTTTAACCTTA
1 AAACTTTTTAAAAATTATATTTTAACC-CA
* * * * *
49466625 AAAATTTTTGAAAATTACATTCTAACCCT
1 AAACTTTTTAAAAATTATATTTTAACCCA
* **
49466654 AAACTTCTCCAAAATTATATTTTAACCCCA
1 AAACTTTTTAAAAATTATATTTTAA-CCCA
* * *
49466684 AAACTTTCTAAAAATTACATTTTGACCC
1 AAACTTTTTAAAAATTATATTTTAACCC
49466712 TTGATTTCAC
Statistics
Matches: 115, Mismatches: 29, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
29 25 0.22
30 89 0.77
31 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.40
Consensus pattern (29 bp):
AAACTTTTTAAAAATTATATTTTAACCCA
Found at i:49466601 original size:60 final size:59
Alignment explanation
Indices: 49466530--49466711 Score: 231
Period size: 60 Copynumber: 3.1 Consensus size: 59
49466520 ACCCTAGAAG
** * *
49466530 CCCCTAAACTTTTTGAAAATTATATTTTGACTCCAAAACTTTTTAAAAATTATATTTTGA
1 CCCCTAAACTTTTCCAAAATTATATTTTAAC-CCAAAACTTTTTAAAAATTACATTTTGA
* * * *
49466590 CCCCTAAACTTTTCCAAAATTATATTTTAACCTTAAAAATTTTTGAAAATTACATTCT-A
1 CCCCTAAACTTTTCCAAAATTATATTTTAACC-CAAAACTTTTTAAAAATTACATTTTGA
* * *
49466649 ACCCTAAACTTCTCCAAAATTATATTTTAACCCCAAAACTTTCTAAAAATTACATTTTGA
1 CCCCTAAACTTTTCCAAAATTATATTTTAA-CCCAAAACTTTTTAAAAATTACATTTTGA
49466709 CCC
1 CCC
49466712 TTGATTTCAC
Statistics
Matches: 103, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
59 50 0.49
60 53 0.51
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.39
Consensus pattern (59 bp):
CCCCTAAACTTTTCCAAAATTATATTTTAACCCAAAACTTTTTAAAAATTACATTTTGA
Found at i:49466698 original size:89 final size:90
Alignment explanation
Indices: 49466539--49466706 Score: 214
Period size: 89 Copynumber: 1.9 Consensus size: 90
49466529 GCCCCTAAAC
* * * * * * *
49466539 TTTTTGAAAATTATATTTTGACTCCAAAACTTTTTAAAAATTATATTTTGACCCCTAAACTTTTC
1 TTTTTGAAAATTACATTCTAACTCCAAAACTTCTCAAAAATTATATTTTAACCCCAAAACTTTTC
* *
49466604 CAAAATTATATTTTAACCTTAAAAA
66 AAAAATTACATTTTAACCTTAAAAA
* *
49466629 TTTTTGAAAATTACATTCTAAC-CCTAAACTTCTCCAAAATTATATTTTAACCCCAAAAC-TTTC
1 TTTTTGAAAATTACATTCTAACTCCAAAACTTCTCAAAAATTATATTTTAACCCCAAAACTTTTC
49466692 TAAAAATTACATTTT
66 -AAAAATTACATTTT
49466707 GACCCTTGAT
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
88 4 0.06
89 43 0.65
90 19 0.29
ACGTcount: A:0.39, C:0.17, G:0.02, T:0.42
Consensus pattern (90 bp):
TTTTTGAAAATTACATTCTAACTCCAAAACTTCTCAAAAATTATATTTTAACCCCAAAACTTTTC
AAAAATTACATTTTAACCTTAAAAA
Found at i:49466725 original size:59 final size:60
Alignment explanation
Indices: 49466545--49466829 Score: 228
Period size: 59 Copynumber: 4.8 Consensus size: 60
49466535 AAACTTTTTG
* * * * * *
49466545 AAAATTATATTTTGACTCCAAAACTTTTTAAAAATTATATTTTGACCCCTAAACTTT-TCC
1 AAAATTATATTTTAACCCCAAAACTTTCTAAAAATTACATTTT-AACCCTAAACTTTCACC
** * * * * *
49466605 AAAATTATATTTTAACCTTAAAAATTTTTGAAAATTACATTCTAACCCTAAAC-TTCTCC
1 AAAATTATATTTTAACCCCAAAACTTTCTAAAAATTACATTTTAACCCTAAACTTTCACC
* **
49466664 AAAATTATATTTTAACCCCAAAACTTTCTAAAAATTACATTTTGACCCTTGA-TTTCACC
1 AAAATTATATTTTAACCCCAAAACTTTCTAAAAATTACATTTTAACCCTAAACTTTCACC
* * * * * * *
49466723 AAAATTACCATTTT-ACCCCTAAACTTTCT-AAAATTTCATTTTAACCCT-GATTTTAACA
1 AAAATTA-TATTTTAACCCCAAAACTTTCTAAAAATTACATTTTAACCCTAAACTTTCACC
* * *
49466781 AAAATTACTATTTT-ACCCTC-GAACCTTCT-AAAATTCCATTTTTAACCCT
1 AAAATTA-TATTTTAACCC-CAAAACTTTCTAAAAATTACA-TTTTAACCCT
49466830 GATTTTTTCT
Statistics
Matches: 190, Mismatches: 29, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
57 2 0.01
58 56 0.29
59 92 0.48
60 40 0.21
ACGTcount: A:0.37, C:0.21, G:0.02, T:0.39
Consensus pattern (60 bp):
AAAATTATATTTTAACCCCAAAACTTTCTAAAAATTACATTTTAACCCTAAACTTTCACC
Found at i:49466785 original size:58 final size:58
Alignment explanation
Indices: 49466664--49466873 Score: 210
Period size: 59 Copynumber: 3.6 Consensus size: 58
49466654 AAACTTCTCC
* * * * *
49466664 AAAATTA-TATTTTAACCCCAAAACTTTCTAAAAATTACATTTTGACCCTTGA-TTTCACC
1 AAAATTACCATTTT-ACCCCTAAACTTTCT-AAAATTACATTTTAACCC-TGATTTTAACA
*
49466723 AAAATTACCATTTTACCCCTAAACTTTCTAAAATTTCATTTTAACCCTGATTTTAACA
1 AAAATTACCATTTTACCCCTAAACTTTCTAAAATTACATTTTAACCCTGATTTTAACA
* * * * ** *
49466781 AAAATTACTATTTTA-CCCTCGAACCTTCTAAAATTCCATTTTTAACCCTGATTTTTTCT
1 AAAATTACCATTTTACCCCT-AAACTTTCTAAAATTACA-TTTTAACCCTGATTTTAACA
* * *
49466840 AAAATTACCATTTTACCTCGAAACTTTCCAAAAT
1 AAAATTACCATTTTACCCCTAAACTTTCTAAAAT
49466874 CCCTTTTTGA
Statistics
Matches: 127, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
57 7 0.06
58 50 0.39
59 63 0.50
60 7 0.06
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCTAAACTTTCTAAAATTACATTTTAACCCTGATTTTAACA
Found at i:49466823 original size:29 final size:30
Alignment explanation
Indices: 49466791--49466976 Score: 94
Period size: 29 Copynumber: 6.4 Consensus size: 30
49466781 AAAATTACTA
*
49466791 TTTT-ACCCTCGAACCTTCTAAAATTCCAT
1 TTTTGACCCTCGAACCTTCCAAAATTCCAT
* *** *
49466820 TTTTAACCCT-GATTTTTTCTAAAATTACCA-
1 TTTTGACCCTCGA-ACCTTCCAAAATT-CCAT
* *
49466850 TTTT-A-CCTCGAAACTTTCCAAAA-TCCCT
1 TTTTGACCCTCG-AACCTTCCAAAATTCCAT
*
49466878 TTTTGA-CCTC-AACTTTCCAAAA-TCTCAT
1 TTTTGACCCTCGAACCTTCCAAAATTC-CAT
** *
49466906 TTTTGACCC-CGATTCTACCAAAAATTACC-T
1 TTTTGACCCTCGAACCTTCC-AAAATT-CCAT
*
49466936 TTTT-ACCCTTGAA-CTTCCCAAAATTCCAT
1 TTTTGACCCTCGAACCTT-CCAAAATTCCAT
49466965 TTTTGA-CCTCGA
1 TTTTGACCCTCGA
49466977 TTTTACCAAA
Statistics
Matches: 124, Mismatches: 16, Indels: 34
0.71 0.09 0.20
Matches are distributed among these distances:
27 16 0.13
28 19 0.15
29 49 0.40
30 34 0.27
31 5 0.04
32 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.05, T:0.39
Consensus pattern (30 bp):
TTTTGACCCTCGAACCTTCCAAAATTCCAT
Found at i:49466840 original size:30 final size:30
Alignment explanation
Indices: 49466747--49466853 Score: 87
Period size: 29 Copynumber: 3.6 Consensus size: 30
49466737 ACCCCTAAAC
*
49466747 TTTCTAAAATTTCA-TTTTAACCCTGATTT
1 TTTCTAAAATTCCATTTTTAACCCTGATTT
** * * **
49466776 TAACAAAAATTAC-TATTTT-ACCCTCGA-AC
1 TTTCTAAAATTCCAT-TTTTAACCCT-GATTT
*
49466805 CTTCTAAAATTCCATTTTTAACCCTGATTT
1 TTTCTAAAATTCCATTTTTAACCCTGATTT
49466835 TTTCTAAAATTACCATTTT
1 TTTCTAAAATT-CCATTTT
49466854 ACCTCGAAAC
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
29 28 0.49
30 22 0.39
31 7 0.12
ACGTcount: A:0.32, C:0.21, G:0.03, T:0.45
Consensus pattern (30 bp):
TTTCTAAAATTCCATTTTTAACCCTGATTT
Found at i:49466873 original size:59 final size:59
Alignment explanation
Indices: 49466684--49466881 Score: 208
Period size: 58 Copynumber: 3.4 Consensus size: 59
49466674 TTTAACCCCA
* * * * * *
49466684 AAACTTTCTAAAAATTACA-TTTTGACCCTTGA-TTTCACCAAAATTACCATTTTACCCCT
1 AAACTTTCT-AAAATTCCATTTTTAACCC-TGATTTTAACAAAAATTACCATTTTACCTCG
* *
49466743 AAACTTTCTAAAATTTCA-TTTTAACCCTGATTTTAACAAAAATTACTATTTTACCCTCG
1 AAACTTTCTAAAATTCCATTTTTAACCCTGATTTTAACAAAAATTACCATTTTA-CCTCG
* ** *
49466802 -AACCTTCTAAAATTCCATTTTTAACCCTGATTTTTTCTAAAATTACCATTTTACCTCG
1 AAACTTTCTAAAATTCCATTTTTAACCCTGATTTTAACAAAAATTACCATTTTACCTCG
* *
49466860 AAACTTTCCAAAA-TCCCTTTTT
1 AAACTTTCTAAAATTCCATTTTT
49466882 GACCTCAACT
Statistics
Matches: 119, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
57 3 0.03
58 63 0.53
59 53 0.45
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (59 bp):
AAACTTTCTAAAATTCCATTTTTAACCCTGATTTTAACAAAAATTACCATTTTACCTCG
Found at i:49466891 original size:27 final size:28
Alignment explanation
Indices: 49466861--49466913 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
49466851 TTTACCTCGA
*
49466861 AACTTTCCAAAATC-CCTTTTTGACCTC
1 AACTTTCCAAAATCTCATTTTTGACCTC
49466888 AACTTTCCAAAATCTCATTTTTGACC
1 AACTTTCCAAAATCTCATTTTTGACC
49466914 CCGATTCTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.28, C:0.30, G:0.04, T:0.38
Consensus pattern (28 bp):
AACTTTCCAAAATCTCATTTTTGACCTC
Found at i:49466939 original size:30 final size:30
Alignment explanation
Indices: 49466905--49466998 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 30
49466895 CAAAATCTCA
49466905 TTTTTGACCCCGATTCTACCAAAAATTACC
1 TTTTTGACCCCGATTCTACCAAAAATTACC
* * * *
49466935 TTTTT-ACCCTTGA-ACTTCCCAAAATT-CC
1 TTTTTGACCC-CGATTCTACCAAAAATTACC
* *
49466963 ATTTTTGACCTCGATTTTACCAAAAATTACC
1 -TTTTTGACCCCGATTCTACCAAAAATTACC
*
49466994 ATTTT
1 TTTTT
49466999 ATCCCCCGAA
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
28 2 0.04
29 21 0.44
30 23 0.48
31 2 0.04
ACGTcount: A:0.29, C:0.27, G:0.05, T:0.39
Consensus pattern (30 bp):
TTTTTGACCCCGATTCTACCAAAAATTACC
Found at i:49466957 original size:59 final size:61
Alignment explanation
Indices: 49466888--49467020 Score: 191
Period size: 59 Copynumber: 2.2 Consensus size: 61
49466878 TTTTGACCTC
* **
49466888 AACTTTCCAAAATCT-CATTTTTGACCCCGATTCTACCAAAAATTACCTTTTTA-CCCTTG
1 AACTTTCCAAAATCTCCATTTTTGACCCCGATTCTACCAAAAATTACCATTTTATCCCCCG
* * *
49466947 AACTTCCCAAAAT-TCCATTTTTGACCTCGATTTTACCAAAAATTACCATTTTATCCCCCG
1 AACTTTCCAAAATCTCCATTTTTGACCCCGATTCTACCAAAAATTACCATTTTATCCCCCG
49467007 AACTTTCCAAAATC
1 AACTTTCCAAAATC
49467021 CCGTTTTAAC
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
58 1 0.02
59 47 0.73
60 16 0.25
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (61 bp):
AACTTTCCAAAATCTCCATTTTTGACCCCGATTCTACCAAAAATTACCATTTTATCCCCCG
Found at i:49466961 original size:145 final size:144
Alignment explanation
Indices: 49466744--49467027 Score: 360
Period size: 145 Copynumber: 2.0 Consensus size: 144
49466734 TTTACCCCTA
* * * *
49466744 AACTTTCTAAAATTTCATTTTAACCCTGATTTTAACAAAAATTACTATTTTACCCTCGAACCTTC
1 AACTTTCCAAAATCTCATTTTAACCCCGATTCTAACAAAAATTACTATTTTACCCTCGAACCTTC
* ** * *
49466809 TAAAATTCCATTTTTAACC-CTGATTTTTTCTAAAATTACCATTTTA-CCTCGAAACTTTCCAAA
66 CAAAATTCCATTTTTAACCTC-GATTTTACCAAAAATTACCATTTTACCCCCG-AACTTTCCAAA
*
49466872 ATCCCTTTTTGACCTC
129 ATCCCGTTTTGACCTC
* * *
49466888 AACTTTCCAAAATCTCATTTTTGACCCCGATTCTACCAAAAATTACCT-TTTTACCCTTGAA-CT
1 AACTTTCCAAAATCTCA-TTTTAACCCCGATTCTAACAAAAATTA-CTATTTTACCCTCGAACCT
*
49466951 TCCCAAAATTCCATTTTTGACCTCGATTTTACCAAAAATTACCATTTTATCCCCCGAACTTTCCA
64 T-CCAAAATTCCATTTTTAACCTCGATTTTACCAAAAATTACCATTTTA-CCCCCGAACTTTCCA
49467016 AAATCCCGTTTT
127 AAATCCCGTTTT
49467028 AACTCAATTT
Statistics
Matches: 120, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
144 18 0.15
145 75 0.62
146 23 0.19
147 4 0.03
ACGTcount: A:0.30, C:0.27, G:0.04, T:0.39
Consensus pattern (144 bp):
AACTTTCCAAAATCTCATTTTAACCCCGATTCTAACAAAAATTACTATTTTACCCTCGAACCTTC
CAAAATTCCATTTTTAACCTCGATTTTACCAAAAATTACCATTTTACCCCCGAACTTTCCAAAAT
CCCGTTTTGACCTC
Found at i:49466985 original size:29 final size:28
Alignment explanation
Indices: 49466810--49466998 Score: 95
Period size: 29 Copynumber: 6.5 Consensus size: 28
49466800 CGAACCTTCT
* *
49466810 AAAATTCCATTTTTAACC-CTGATTTTTTCT
1 AAAATTCCATTTTTGACCTC-GA--TTTTCC
*
49466840 AAAATTACCA-TTTT-ACCTCGAAACTTTCC
1 AAAATT-CCATTTTTGACCTCG--ATTTTCC
* * *
49466869 AAAA-TCCCTTTTTGACCTCAACTTTCC
1 AAAATTCCATTTTTGACCTCGATTTTCC
* *
49466896 AAAA-TCTCATTTTTGACCCCGATTCTACC
1 AAAATTC-CATTTTTGACCTCGATT-TTCC
* * *
49466925 AAAAATTACC-TTTTT-ACCCTTGAACTTCCC
1 -AAAATT-CCATTTTTGA-CCTCG-ATTTTCC
49466955 AAAATTCCATTTTTGACCTCGATTTTACC
1 AAAATTCCATTTTTGACCTCGATTTT-CC
49466984 AAAAATTACCATTTT
1 -AAAATT-CCATTTT
49466999 ATCCCCCGAA
Statistics
Matches: 125, Mismatches: 16, Indels: 35
0.71 0.09 0.20
Matches are distributed among these distances:
27 15 0.12
28 23 0.18
29 38 0.30
30 33 0.26
31 15 0.12
32 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.39
Consensus pattern (28 bp):
AAAATTCCATTTTTGACCTCGATTTTCC
Found at i:49467044 original size:59 final size:59
Alignment explanation
Indices: 49466921--49467060 Score: 160
Period size: 59 Copynumber: 2.4 Consensus size: 59
49466911 ACCCCGATTC
* ** * * *
49466921 TACCAAAAATTACCTTTTTACCCTTGAACTTCCCAAAATTCCATTTTTGACCTCGATTT
1 TACCAAAAATTACCATTTTACCCCCGAACTTCCCAAAATTCCAGTTTTGAACTCAATTT
* *
49466980 TACCAAAAATTACCATTTTATCCCCCGAACTTTCCAAAA-TCCCGTTTT-AACTCAATTT
1 TACCAAAAATTACCATTTTA-CCCCCGAACTTCCCAAAATTCCAGTTTTGAACTCAATTT
*
49467038 TGACC-AAAATTATCATTTTACCC
1 T-ACCAAAAATTACCATTTTACCC
49467061 TCGGGTATCC
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
57 3 0.04
58 23 0.33
59 29 0.41
60 15 0.21
ACGTcount: A:0.31, C:0.28, G:0.04, T:0.36
Consensus pattern (59 bp):
TACCAAAAATTACCATTTTACCCCCGAACTTCCCAAAATTCCAGTTTTGAACTCAATTT
Found at i:49473141 original size:36 final size:35
Alignment explanation
Indices: 49473084--49473153 Score: 90
Period size: 34 Copynumber: 2.0 Consensus size: 35
49473074 TATTTTAGGT
49473084 ATCATTTCGTACAGATCAACAAAAAAAATTAATGTTC
1 ATCATTTCGTACAGATCAAC--AAAAAATTAATGTTC
*
49473121 ATCATTT-GTACA-ATTTAACAAAAAATTAATGTT
1 ATCATTTCGTACAGA-TCAACAAAAAATTAATGTT
49473154 GATATGGGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
34 14 0.45
35 1 0.03
36 9 0.29
37 7 0.23
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (35 bp):
ATCATTTCGTACAGATCAACAAAAAATTAATGTTC
Found at i:49473369 original size:45 final size:45
Alignment explanation
Indices: 49473305--49473391 Score: 174
Period size: 45 Copynumber: 1.9 Consensus size: 45
49473295 CAACTGGGGT
49473305 GGATAAGTTGAACTTATCCAAATTGTCTGGATTAAAAGATGGGAA
1 GGATAAGTTGAACTTATCCAAATTGTCTGGATTAAAAGATGGGAA
49473350 GGATAAGTTGAACTTATCCAAATTGTCTGGATTAAAAGATGG
1 GGATAAGTTGAACTTATCCAAATTGTCTGGATTAAAAGATGG
49473392 ACCATTGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (45 bp):
GGATAAGTTGAACTTATCCAAATTGTCTGGATTAAAAGATGGGAA
Found at i:49474405 original size:28 final size:29
Alignment explanation
Indices: 49474364--49474425 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
49474354 AACACTAAAC
* * * *
49474364 TAATGTTTGTTATAATTTTTACAATTTTT
1 TAATATTTGTTATAATGTTCACAAATTTT
49474393 TAATATTT-TTATAATGTTCACAAATTTT
1 TAATATTTGTTATAATGTTCACAAATTTT
*
49474421 AAATA
1 TAATA
49474426 ATTCTTAAGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 21 0.75
29 7 0.25
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (29 bp):
TAATATTTGTTATAATGTTCACAAATTTT
Found at i:49483578 original size:25 final size:25
Alignment explanation
Indices: 49483508--49483597 Score: 99
Period size: 25 Copynumber: 3.6 Consensus size: 25
49483498 AATTCTATTT
* * * *
49483508 TGGCTCGTAAGAGCAATATATTATC
1 TGGCTCGTAAGAGCGACATTTTGTC
49483533 TGGCTCGTAAGAGCGACATTTTGTC
1 TGGCTCGTAAGAGCGACATTTTGTC
* **
49483558 TGGCTCGTAAGAGTGTGATTTTGTC
1 TGGCTCGTAAGAGCGACATTTTGTC
*
49483583 TGGGCTCGTATGAGC
1 T-GGCTCGTAAGAGC
49483598 TATATATTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
25 44 0.80
26 11 0.20
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.33
Consensus pattern (25 bp):
TGGCTCGTAAGAGCGACATTTTGTC
Found at i:49488489 original size:27 final size:27
Alignment explanation
Indices: 49488444--49488517 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
49488434 GAGACTCTAC
* * *
49488444 TTATTGCTCGAGTATAGCTTCGACCTG
1 TTATAGCTCGGGTAGAGCTTCGACCTG
*
49488471 TTATAGCTCGGGTAGAGCTTCGACTTG
1 TTATAGCTCGGGTAGAGCTTCGACCTG
49488498 TTATAGCTCGGGTAGAGCTT
1 TTATAGCTCGGGTAGAGCTT
49488518 TGGTTTACTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (27 bp):
TTATAGCTCGGGTAGAGCTTCGACCTG
Found at i:49488567 original size:55 final size:54
Alignment explanation
Indices: 49488498--49488679 Score: 217
Period size: 55 Copynumber: 3.4 Consensus size: 54
49488488 CTTCGACTTG
* * ** *
49488498 TTATAGCTCGGGTAGAGCTTTGGTTTACTTACATCTCAGTTTGAGCGTAAAGCTT
1 TTATAGCTCTGGTAGAGCTTCGAATTACTTACATCTCA-TTAGAGCGTAAAGCTT
* * *
49488553 TTATAGCTCAGGTAGAGCTTCGAACTACTTACA--TCATTAGAGCGTAAAACTT
1 TTATAGCTCTGGTAGAGCTTCGAATTACTTACATCTCATTAGAGCGTAAAGCTT
* * *
49488605 TTATAGCT-TGAGTAGAGCTTCGAATTGCTTACGTCTCAATTAGAGCGTAAAGCTA
1 TTATAGCTCTG-GTAGAGCTTCGAATTACTTACATCTC-ATTAGAGCGTAAAGCTT
49488660 TTATAGCTCTGGTAGAGCTT
1 TTATAGCTCTGGTAGAGCTT
49488680 TGTTCTAGTT
Statistics
Matches: 109, Mismatches: 13, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
51 1 0.01
52 41 0.38
53 3 0.03
54 2 0.02
55 60 0.55
56 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (54 bp):
TTATAGCTCTGGTAGAGCTTCGAATTACTTACATCTCATTAGAGCGTAAAGCTT
Found at i:49488620 original size:52 final size:54
Alignment explanation
Indices: 49488540--49488679 Score: 171
Period size: 52 Copynumber: 2.6 Consensus size: 54
49488530 ATCTCAGTTT
*
49488540 GAGCGTAAAGCTTTTATAGC-TCAGGTAGAGCTTCGAACTACTTAC-ATC-ATTA
1 GAGCGTAAAGCTTTTATAGCTTGA-GTAGAGCTTCGAACTACTTACGATCAATTA
* * * *
49488592 GAGCGTAAAACTTTTATAGCTTGAGTAGAGCTTCGAATTGCTTACGTCTCAATTA
1 GAGCGTAAAGCTTTTATAGCTTGAGTAGAGCTTCGAACTACTTACG-ATCAATTA
*
49488647 GAGCGTAAAGCTATTATAGCTCTG-GTAGAGCTT
1 GAGCGTAAAGCTTTTATAGCT-TGAGTAGAGCTT
49488680 TGTTCTAGTT
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
52 38 0.50
53 2 0.03
54 2 0.03
55 32 0.42
56 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Consensus pattern (54 bp):
GAGCGTAAAGCTTTTATAGCTTGAGTAGAGCTTCGAACTACTTACGATCAATTA
Found at i:49488692 original size:55 final size:54
Alignment explanation
Indices: 49488498--49488723 Score: 190
Period size: 55 Copynumber: 4.2 Consensus size: 54
49488488 CTTCGACTTG
* * * * * * *
49488498 TTATAGCTCGGGTAGAGCTTTGGTTTACTTACATCTCAGTTTGAGCGTAAAGCTT
1 TTATAGCTCTGGTAGAGC-TTCGATTACTTACGTCTCAATTAGAGCGTAAAGCTA
* * * * *
49488553 TTATAGCTCAGGTAGAGCTTCGAACTACTTAC--ATC-ATTAGAGCGTAAAACTT
1 TTATAGCTCTGGTAGAGCTTCG-ATTACTTACGTCTCAATTAGAGCGTAAAGCTA
*
49488605 TTATAGCT-TGAGTAGAGCTTCGAATTGCTTACGTCTCAATTAGAGCGTAAAGCTA
1 TTATAGCTCTG-GTAGAGCTTCG-ATTACTTACGTCTCAATTAGAGCGTAAAGCTA
* * * * ** *
49488660 TTATAGCTCTGGTAGAGCTTTGTTCTAGTTACGTGTCGGTTAGAGCATAAAGCTA
1 TTATAGCTCTGGTAGAGCTTCGAT-TACTTACGTCTCAATTAGAGCGTAAAGCTA
*
49488715 TTCTAGCTC
1 TTATAGCTC
49488724 AAGAGGAGTT
Statistics
Matches: 141, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
51 1 0.01
52 41 0.29
53 2 0.01
54 6 0.04
55 89 0.63
56 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (54 bp):
TTATAGCTCTGGTAGAGCTTCGATTACTTACGTCTCAATTAGAGCGTAAAGCTA
Found at i:49494038 original size:28 final size:28
Alignment explanation
Indices: 49494006--49494095 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 28
49493996 ACAGCTCGGG
49494006 TAGAGCTTTGAAAGGCTTACATCTTGGT
1 TAGAGCTTTGAAAGGCTTACATCTTGGT
* * * * * * *
49494034 TAGAGC-GT-AATGTGATGTATAGCTCGGG
1 TAGAGCTTTGAAAG-GCT-TACATCTTGGT
*
49494062 TAGAGCTTTGGAAGGCTTACATCTTGGT
1 TAGAGCTTTGAAAGGCTTACATCTTGGT
49494090 TAGAGC
1 TAGAGC
49494096 GTAATGTGAT
Statistics
Matches: 43, Mismatches: 15, Indels: 8
0.65 0.23 0.12
Matches are distributed among these distances:
26 3 0.07
27 3 0.07
28 32 0.74
29 3 0.07
30 2 0.05
ACGTcount: A:0.24, C:0.13, G:0.30, T:0.32
Consensus pattern (28 bp):
TAGAGCTTTGAAAGGCTTACATCTTGGT
Found at i:49494071 original size:56 final size:56
Alignment explanation
Indices: 49493946--49494175 Score: 281
Period size: 56 Copynumber: 4.2 Consensus size: 56
49493936 CTTCGACGGG
* * * *
49493946 CAGCTCGGGTTGAGCTTTGAAAGGTTTACGTCTCGGTTAGA--G---TGCAATGTA
1 CAGCTCGGGTAGAGCTTTGAAAGGCTTACATCTCGGTTAGAGCGTAATGCGATGTA
* *
49493997 CAGCTCGGGTAGAGCTTTGAAAGGCTTACATCTTGGTTAGAGCGTAATGTGATGTA
1 CAGCTCGGGTAGAGCTTTGAAAGGCTTACATCTCGGTTAGAGCGTAATGCGATGTA
* * * *
49494053 TAGCTCGGGTAGAGCTTTGGAAGGCTTACATCTTGGTTAGAGCGTAATGTGATGTA
1 CAGCTCGGGTAGAGCTTTGAAAGGCTTACATCTCGGTTAGAGCGTAATGCGATGTA
* * * * *
49494109 CAGCTCGAGTAGAGCTTTGGAAGGCTTACATCTCGATTAGAGCATAATACGATGTA
1 CAGCTCGGGTAGAGCTTTGAAAGGCTTACATCTCGGTTAGAGCGTAATGCGATGTA
*
49494165 TAGCTCGGGTA
1 CAGCTCGGGTA
49494176 AATATATGGT
Statistics
Matches: 157, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
51 37 0.24
53 1 0.01
56 119 0.76
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (56 bp):
CAGCTCGGGTAGAGCTTTGAAAGGCTTACATCTCGGTTAGAGCGTAATGCGATGTA
Found at i:49494110 original size:28 final size:28
Alignment explanation
Indices: 49494023--49494110 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
49494013 TTGAAAGGCT
49494023 TACATCTTGGTTAGAGCGTAATGTGATG
1 TACATCTTGGTTAGAGCGTAATGTGATG
* * * * * *
49494051 TATAGCTCGGGTAGAGC-T-TTG-GAAGG
1 TACATCTTGGTTAGAGCGTAATGTG-ATG
49494077 CTTACATCTTGGTTAGAGCGTAATGTGATG
1 --TACATCTTGGTTAGAGCGTAATGTGATG
49494107 TACA
1 TACA
49494111 GCTCGAGTAG
Statistics
Matches: 42, Mismatches: 12, Indels: 12
0.64 0.18 0.18
Matches are distributed among these distances:
25 1 0.02
26 4 0.10
27 1 0.02
28 30 0.71
29 1 0.02
30 4 0.10
31 1 0.02
ACGTcount: A:0.25, C:0.12, G:0.30, T:0.33
Consensus pattern (28 bp):
TACATCTTGGTTAGAGCGTAATGTGATG
Found at i:49494209 original size:112 final size:112
Alignment explanation
Indices: 49493992--49494211 Score: 260
Period size: 112 Copynumber: 2.0 Consensus size: 112
49493982 TTAGAGTGCA
* * * * **
49493992 ATGTACAGCTCGGGTAGAGCTTTGAAAGGCTTACATCTTGGTTAGAGCGTAATGTGATGTATAGC
1 ATGTACAGCTCGAGTAGAGCTTTGAAAGGCTTACATCTCGATTAGAGCATAATACGATGTATAGC
* * * * * * *
49494057 TCGGGTAGAGCTTTGGAAGGCTTACATCTTGGTTAGAGCGTAATGTG
66 TCGGGTAAAGATATGGAAGACTTACATCTCGATTAAAGCGTAATGTG
*
49494104 ATGTACAGCTCGAGTAGAGCTTTGGAAGGCTTACATCTCGATTAGAGCATAATACGATGTATAGC
1 ATGTACAGCTCGAGTAGAGCTTTGAAAGGCTTACATCTCGATTAGAGCATAATACGATGTATAGC
* *** **
49494169 TCGGGTAAATATATGGTTTACTTATGTCTCGATTAAAGCGTAA
66 TCGGGTAAAGATATGGAAGACTTACATCTCGATTAAAGCGTAA
49494212 GGTTACTTCA
Statistics
Matches: 88, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
112 88 1.00
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.31
Consensus pattern (112 bp):
ATGTACAGCTCGAGTAGAGCTTTGAAAGGCTTACATCTCGATTAGAGCATAATACGATGTATAGC
TCGGGTAAAGATATGGAAGACTTACATCTCGATTAAAGCGTAATGTG
Found at i:49497976 original size:27 final size:27
Alignment explanation
Indices: 49497937--49498045 Score: 96
Period size: 27 Copynumber: 4.0 Consensus size: 27
49497927 GAGACTTTGC
*
49497937 TTATAGCTCGGGTAGAGCTTCGACCTG
1 TTATAGCTCGGGTAGAGCTTCGAACTG
* *
49497964 TTATAGCTTGGGTAGAGCTTTGAACTG
1 TTATAGCTCGGGTAGAGCTTCGAACTG
* * * * *
49497991 TT-TACGTCTCTGTTAGAGCGT-AAAGCTT
1 TTATA-G-CTCGGGTAGAGCTTCGAA-CTG
*
49498019 TTATAGCCCGGGTAGAGCTTCGAACTG
1 TTATAGCTCGGGTAGAGCTTCGAACTG
49498046 CTTACATCTC
Statistics
Matches: 62, Mismatches: 15, Indels: 10
0.71 0.17 0.11
Matches are distributed among these distances:
26 2 0.03
27 41 0.66
28 17 0.27
29 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (27 bp):
TTATAGCTCGGGTAGAGCTTCGAACTG
Found at i:49498023 original size:55 final size:55
Alignment explanation
Indices: 49497964--49498130 Score: 210
Period size: 55 Copynumber: 3.0 Consensus size: 55
49497954 CTTCGACCTG
* * * *
49497964 TTATAGCTTGGGTAGAGCTTTGAACTGTTTACGTCTCTGTTAGAGCGTAAAGCTT
1 TTATAGCTTGGGTAGAGCTTTGAACTGCTTACATCTCGGTTAGAGCGTAAAGCTA
** * *
49498019 TTATAGCCCGGGTAGAGCTTCGAACTGCTTACATCTCGGTTAAAGCGTAAAGCTA
1 TTATAGCTTGGGTAGAGCTTTGAACTGCTTACATCTCGGTTAGAGCGTAAAGCTA
* ** *
49498074 TTATAGCTCT-GATAGAGCTTTGGTCTGCTTACATCTCGGTTAGAGCTTAAAGCTA
1 TTATAGCT-TGGGTAGAGCTTTGAACTGCTTACATCTCGGTTAGAGCGTAAAGCTA
49498129 TT
1 TT
49498131 CCAACTCAAA
Statistics
Matches: 95, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
55 95 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (55 bp):
TTATAGCTTGGGTAGAGCTTTGAACTGCTTACATCTCGGTTAGAGCGTAAAGCTA
Found at i:49501434 original size:10 final size:10
Alignment explanation
Indices: 49501421--49501504 Score: 52
Period size: 10 Copynumber: 8.8 Consensus size: 10
49501411 TTTTAATCAA
*
49501421 TTTTATAATT
1 TTTTAAAATT
49501431 TTTTAAAA--
1 TTTTAAAATT
49501439 TTTT-AAATT
1 TTTTAAAATT
*
49501448 TGTTTACAATT
1 T-TTTAAAATT
* *
49501459 TATTAATA-T
1 TTTTAAAATT
* *
49501468 TTTCACAATT
1 TTTTAAAATT
*
49501478 TTTTAAACTT
1 TTTTAAAATT
*
49501488 TTTT-ACATT
1 TTTTAAAATT
49501497 TTTTAAAA
1 TTTTAAAA
49501505 ACGATTTTTT
Statistics
Matches: 53, Mismatches: 15, Indels: 12
0.66 0.19 0.15
Matches are distributed among these distances:
7 3 0.06
8 4 0.08
9 13 0.25
10 28 0.53
11 5 0.09
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.58
Consensus pattern (10 bp):
TTTTAAAATT
Found at i:49501440 original size:18 final size:18
Alignment explanation
Indices: 49501419--49501459 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
49501409 AATTTTAATC
49501419 AATTTTATAATTT-TTTAA
1 AATTTTA-AATTTGTTTAA
*
49501437 AATTTTAAATTTGTTTAC
1 AATTTTAAATTTGTTTAA
49501455 AATTT
1 AATTT
49501460 ATTAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (18 bp):
AATTTTAAATTTGTTTAA
Found at i:49501453 original size:28 final size:28
Alignment explanation
Indices: 49501421--49501492 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 28
49501411 TTTTAATCAA
49501421 TTTTATAATTTTTTAAAATTTT-A-AATT
1 TTTTA-AATTTTTTAAAATTTTCACAATT
* *
49501448 TGTTTACAATTTATTAATATTTTCACAATT
1 T-TTTA-AATTTTTTAAAATTTTCACAATT
49501478 TTTTAAACTTTTTTA
1 TTTTAAA-TTTTTTA
49501493 CATTTTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
27 1 0.03
28 20 0.54
29 11 0.30
30 5 0.14
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (28 bp):
TTTTAAATTTTTTAAAATTTTCACAATT
Found at i:49501489 original size:19 final size:18
Alignment explanation
Indices: 49501403--49501503 Score: 64
Period size: 19 Copynumber: 5.4 Consensus size: 18
49501393 TCTTTAGTAA
*
49501403 TTTTACAATTTTAATCAATT
1 TTTTA-AATTTTTA-CAATT
* * *
49501423 TTATAATTTTTTA-AA-A
1 TTTTAAATTTTTACAATT
49501439 TTTTAAATTTGTTTACAATT
1 TTTTAAA-TT-TTTACAATT
* *
49501459 TATTAATATTTTCACAATT
1 TTTTAA-ATTTTTACAATT
49501478 TTTTAAACTTTTTTAC-ATT
1 TTTTAAA--TTTTTACAATT
49501497 TTTTAAA
1 TTTTAAA
49501504 AACGATTTTT
Statistics
Matches: 63, Mismatches: 11, Indels: 15
0.71 0.12 0.17
Matches are distributed among these distances:
16 5 0.08
17 4 0.06
18 5 0.08
19 31 0.49
20 17 0.27
21 1 0.02
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.57
Consensus pattern (18 bp):
TTTTAAATTTTTACAATT
Found at i:49502213 original size:18 final size:18
Alignment explanation
Indices: 49502155--49502213 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
49502145 TTAAACTGTA
* * *
49502155 AAAGAATATTAAAATTTT
1 AAAGATTATTAAAAATAT
49502173 AAA-ATTTATTAAAAAGTTAT
1 AAAGA-TTATTAAAAA--TAT
49502193 AAAGATTATTAAAAATAT
1 AAAGATTATTAAAAATAT
49502211 AAA
1 AAA
49502214 TTTGTAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
17 1 0.03
18 17 0.50
20 15 0.44
21 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (18 bp):
AAAGATTATTAAAAATAT
Found at i:49502241 original size:21 final size:19
Alignment explanation
Indices: 49502203--49502241 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
49502193 AAAGATTATT
*
49502203 AAAAATATAAATTTGTAAA
1 AAAAATATAAAATTGTAAA
49502222 AAAAATTATAAAAATTGTAA
1 AAAAA-TAT-AAAATTGTAA
49502242 TTTTAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 3 0.18
21 9 0.53
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
AAAAATATAAAATTGTAAA
Found at i:49502505 original size:99 final size:99
Alignment explanation
Indices: 49502334--49502532 Score: 373
Period size: 99 Copynumber: 2.0 Consensus size: 99
49502324 CGATATTGTC
*
49502334 ACCGCACAGTTGAAAAAGACATGACAAGTGGGATTTTTCAGACCATGCTTTTCCCTCCCACCATA
1 ACCGCACAGTTGAAAAAGACATGACAAGTGGGAGTTTTCAGACCATGCTTTTCCCTCCCACCATA
49502399 ACCCCTTCACTGCCGACACTCTTTAACGCCAATG
66 ACCCCTTCACTGCCGACACTCTTTAACGCCAATG
49502433 ACCGCACAGTTGAAAAAGACATGA-ACAGTGGGAGTTTTCAGACCATGCTTTTCCCTCCCACCAT
1 ACCGCACAGTTGAAAAAGACATGACA-AGTGGGAGTTTTCAGACCATGCTTTTCCCTCCCACCAT
49502497 AACCCCTTCACTGCCGACACTCTTTAACGCCAATG
65 AACCCCTTCACTGCCGACACTCTTTAACGCCAATG
49502532 A
1 A
49502533 ACTGGCGTTT
Statistics
Matches: 98, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
98 1 0.01
99 97 0.99
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.24
Consensus pattern (99 bp):
ACCGCACAGTTGAAAAAGACATGACAAGTGGGAGTTTTCAGACCATGCTTTTCCCTCCCACCATA
ACCCCTTCACTGCCGACACTCTTTAACGCCAATG
Found at i:49507070 original size:43 final size:43
Alignment explanation
Indices: 49507022--49507105 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
49507012 TTAACATGTG
* *
49507022 GAACTTGTGTGCAATGTGGATTGGAGAAAATATTATTTTATGC
1 GAACTTGTGTGCAATGTGGATTGGAGAAAAAACTATTTTATGC
*
49507065 GAACTTGTGTGCCATGTGGATTGGAGAAAAAACTATTTTAT
1 GAACTTGTGTGCAATGTGGATTGGAGAAAAAACTATTTTAT
49507106 ACAGCATGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (43 bp):
GAACTTGTGTGCAATGTGGATTGGAGAAAAAACTATTTTATGC
Found at i:49511322 original size:3 final size:3
Alignment explanation
Indices: 49511308--49511359 Score: 95
Period size: 3 Copynumber: 17.0 Consensus size: 3
49511298 TGATACTTAA
49511308 ATT ATAT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
49511354 ATT ATT
1 ATT ATT
49511360 TGAGTGCCTA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:49511557 original size:16 final size:16
Alignment explanation
Indices: 49511536--49511576 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
49511526 TTCTTTCTTT
*
49511536 ATATAATAATTAAAAA
1 ATATAAAAATTAAAAA
49511552 ATATAAAAATTAAAAA
1 ATATAAAAATTAAAAA
*
49511568 CTATAAAAA
1 ATATAAAAA
49511577 ATCAATTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATATAAAAATTAAAAA
Found at i:49512511 original size:11 final size:11
Alignment explanation
Indices: 49512489--49512519 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
49512479 TTTTCCTCTA
49512489 TTGTTG-TTTG
1 TTGTTGTTTTG
49512499 TTGTTGTTTTG
1 TTGTTGTTTTG
49512510 TTGTTGTTTT
1 TTGTTGTTTT
49512520 AGTACAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.00, C:0.00, G:0.26, T:0.74
Consensus pattern (11 bp):
TTGTTGTTTTG
Found at i:49512592 original size:22 final size:22
Alignment explanation
Indices: 49512542--49512592 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
49512532 TTTATATTGC
* *
49512542 TATTATTTTATTATTATTATTT
1 TATTATTGTATAATTATTATTT
* * *
49512564 GAATATTGTATAATTCTTATTT
1 TATTATTGTATAATTATTATTT
49512586 TATTATT
1 TATTATT
49512593 AAAGCTATTT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (22 bp):
TATTATTGTATAATTATTATTT
Found at i:49512710 original size:16 final size:16
Alignment explanation
Indices: 49512689--49512730 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
49512679 ATATATTTTA
49512689 ATATTTTTAATATATT
1 ATATTTTTAATATATT
49512705 ATATTTTTAA-A-ATT
1 ATATTTTTAATATATT
49512719 -TATTTTT-ATATA
1 ATATTTTTAATATA
49512731 AAAATAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 1 0.04
13 8 0.33
14 4 0.17
15 1 0.04
16 10 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATATTTTTAATATATT
Found at i:49527236 original size:17 final size:17
Alignment explanation
Indices: 49527203--49527237 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
49527193 ATTGTTTATT
* *
49527203 TCTTTTATATAATTTAA
1 TCTTTTATACAAATTAA
49527220 TCTTTTATACAAATTAA
1 TCTTTTATACAAATTAA
49527237 T
1 T
49527238 AATTTGGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (17 bp):
TCTTTTATACAAATTAA
Found at i:49528399 original size:21 final size:22
Alignment explanation
Indices: 49528350--49528400 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
49528340 ACTATCGTGC
*
49528350 TATAAAAACAGACATAACTGTAT
1 TATAAAAACAAACATAAC-GTAT
49528373 TATAAAAACAAACATAAC-TAT
1 TATAAAAACAAACATAACGTAT
*
49528394 TTTAAAA
1 TATAAAA
49528401 CTTACTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 9 0.35
23 17 0.65
ACGTcount: A:0.57, C:0.12, G:0.04, T:0.27
Consensus pattern (22 bp):
TATAAAAACAAACATAACGTAT
Found at i:49528962 original size:21 final size:21
Alignment explanation
Indices: 49528931--49528970 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
49528921 AAAAGAAAAA
49528931 ACTTGGGGTTTTATATGGAATT
1 ACTTGGGGTTTTAT-TGGAATT
49528953 ACTT-GGGTTTTATTGGAA
1 ACTTGGGGTTTTATTGGAA
49528971 AAACTTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.23, C:0.05, G:0.28, T:0.45
Consensus pattern (21 bp):
ACTTGGGGTTTTATTGGAATT
Found at i:49528976 original size:20 final size:21
Alignment explanation
Indices: 49528927--49528977 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
49528917 AAGAAAAAGA
49528927 AAAAACTTGGGGTTTTATATGG
1 AAAAACTT-GGGTTTTATATGG
**
49528949 AATTACTTGGGTTTTAT-TGG
1 AAAAACTTGGGTTTTATATGG
49528969 AAAAACTTG
1 AAAAACTTG
49528978 AATTTTTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 10 0.40
21 9 0.36
22 6 0.24
ACGTcount: A:0.31, C:0.06, G:0.24, T:0.39
Consensus pattern (21 bp):
AAAAACTTGGGTTTTATATGG
Found at i:49546784 original size:17 final size:17
Alignment explanation
Indices: 49546762--49546800 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
49546752 CTCCACCTTG
* *
49546762 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
49546779 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
49546796 ACAAG
1 ACAAG
49546801 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:49552911 original size:232 final size:230
Alignment explanation
Indices: 49552454--49552918 Score: 885
Period size: 232 Copynumber: 2.0 Consensus size: 230
49552444 TGATTAAATC
49552454 ACAAATTAGTACAAAACACTTCCTTCATCTTATAATTTTTAACCCACGCAAATGTAGAGTTCAAA
1 ACAAATTAGTACAAAACACTTCCTTCATCTTATAATTTTTAACCCACGCAAATGTAGAGTTCAAA
49552519 TGATAGATATGTATAATTCACGTAAAGTTATGATCATGCAATTCAGATATCGGAATATTAATATT
66 TGATAGATATGTATAATTCACGTAAAGTTATGATCATGCAATTCAGATATCGGAATATTAATATT
*
49552584 CAGAATAACCATCACATACATATATCTAGAATTTATTTAAAATCATGAAATAGCAAATTATACAG
131 CAGAATAACCATCACATACATATATCTAGAATTTATTTAAAATCATGAAATAGCAAATGATACAG
49552649 TTCAATTCAATTTATACATATCCTACGAATGACAT
196 TTCAATTCAATTTATACATATCCTACGAATGACAT
49552684 ACAAATTAGTACAAAACACTTCCTTCATCTTATAATTTTTAACCCACGCAAATGTAGAGTTCAAA
1 ACAAATTAGTACAAAACACTTCCTTCATCTTATAATTTTTAACCCACGCAAATGTAGAGTTCAAA
*
49552749 TGATAGATATGTATAATTCACGTAAAGTTATGATCATGCAGTTCAGATATATCGGAATATTAATA
66 TGATAGATATGTATAATTCACGTAAAGTTATGATCATGCAATTCAG--ATATCGGAATATTAATA
49552814 TTCAGAATAACCATCACATACATATATCTAGAATTTATTTAAAATCATGAAATAGCAAATGATAC
129 TTCAGAATAACCATCACATACATATATCTAGAATTTATTTAAAATCATGAAATAGCAAATGATAC
*
49552879 AGTTCAATTCAATTTATACATATCCTACGAATGACTT
194 AGTTCAATTCAATTTATACATATCCTACGAATGACAT
49552916 ACA
1 ACA
49552919 TTCACCTCGC
Statistics
Matches: 230, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
230 110 0.48
232 120 0.52
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (230 bp):
ACAAATTAGTACAAAACACTTCCTTCATCTTATAATTTTTAACCCACGCAAATGTAGAGTTCAAA
TGATAGATATGTATAATTCACGTAAAGTTATGATCATGCAATTCAGATATCGGAATATTAATATT
CAGAATAACCATCACATACATATATCTAGAATTTATTTAAAATCATGAAATAGCAAATGATACAG
TTCAATTCAATTTATACATATCCTACGAATGACAT
Found at i:49554065 original size:30 final size:30
Alignment explanation
Indices: 49554022--49554090 Score: 102
Period size: 30 Copynumber: 2.2 Consensus size: 30
49554012 CATCTAATAG
49554022 GCAAACCCCCTTGCATGCAAAACCCTATAA
1 GCAAACCCCCTTGCATGCAAAACCCTATAA
* *
49554052 GCAAATCCTCTTGCATGCAAAACCCTATAAA
1 GCAAACCCCCTTGCATGCAAAACCCTAT-AA
49554083 TGCAAACC
1 -GCAAACC
49554091 TGTATAGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 26 0.76
31 2 0.06
32 6 0.18
ACGTcount: A:0.38, C:0.33, G:0.10, T:0.19
Consensus pattern (30 bp):
GCAAACCCCCTTGCATGCAAAACCCTATAA
Found at i:49554169 original size:54 final size:54
Alignment explanation
Indices: 49554105--49554212 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
49554095 TAGGAATTAG
* *
49554105 TGTGCGAGCTCTTAAGATAATCCTGCGAACCTAGTTATAGGTGAACCTCTTATA
1 TGTGCGAGCTCTTAAGATAATCATGCAAACCTAGTTATAGGTGAACCTCTTATA
*
49554159 TGTGCGAGCTCTTAAGATAATCATGCAAACCTGGTTATAGGTGAACCTCTTATA
1 TGTGCGAGCTCTTAAGATAATCATGCAAACCTAGTTATAGGTGAACCTCTTATA
49554213 CCTTTAGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (54 bp):
TGTGCGAGCTCTTAAGATAATCATGCAAACCTAGTTATAGGTGAACCTCTTATA
Found at i:49554380 original size:15 final size:14
Alignment explanation
Indices: 49554360--49554451 Score: 53
Period size: 15 Copynumber: 6.4 Consensus size: 14
49554350 AGCATGCGAA
49554360 CCCTAATGTGCAAAC
1 CCCTAA-GTGCAAAC
*
49554375 CCCTAAGTACAAA-
1 CCCTAAGTGCAAAC
*
49554388 CCCTAATGTGCGAAC
1 CCCTAA-GTGCAAAC
** *
49554403 CTTTAAGGTGCGAAC
1 CCCTAA-GTGCAAAC
* *
49554418 TCTTAGAGTGCAAA-
1 CCCTA-AGTGCAAAC
*
49554432 CCCTAAGGTGCGAAC
1 CCCTAA-GTGCAAAC
49554447 CCCTA
1 CCCTA
49554452 GGTGTACGAA
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
13 7 0.12
14 20 0.33
15 32 0.53
16 1 0.02
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (14 bp):
CCCTAAGTGCAAAC
Found at i:49554403 original size:14 final size:13
Alignment explanation
Indices: 49554354--49554448 Score: 64
Period size: 14 Copynumber: 6.7 Consensus size: 13
49554344 AATGTCAGCA
49554354 TGCGAACCCTAATG
1 TGCGAACCCTAA-G
*
49554368 TGCAAACCCCTAAG
1 TGCGAA-CCCTAAG
* *
49554382 TACAAACCCTAATG
1 TGCGAACCCTAA-G
*
49554396 TGCGAACCTTTAAGG
1 TGCGAACC-CTAA-G
*
49554411 TGCGAACTCTTAGAG
1 TGCGAAC-CCTA-AG
*
49554426 TGCAAACCCTAAGG
1 TGCGAACCCTAA-G
49554440 TGCGAACCC
1 TGCGAACCC
49554449 CTAGGTGTAC
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
13 7 0.11
14 30 0.45
15 27 0.41
16 2 0.03
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (13 bp):
TGCGAACCCTAAG
Found at i:49555940 original size:19 final size:17
Alignment explanation
Indices: 49555899--49555943 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
49555889 TGTTTCTTAT
*
49555899 AAATTTTACAATTTTTA
1 AAATTTTACAATTTTCA
49555916 ATAATTGTTACAATTTTCA
1 A-AATT-TTACAATTTTCA
49555935 CAAATTTTA
1 -AAATTTTA
49555944 AAAATTTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 1 0.04
18 7 0.29
19 15 0.62
20 1 0.04
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (17 bp):
AAATTTTACAATTTTCA
Found at i:49555989 original size:58 final size:59
Alignment explanation
Indices: 49555898--49556008 Score: 136
Period size: 58 Copynumber: 1.9 Consensus size: 59
49555888 ATGTTTCTTA
*
49555898 TAAATTTTACAATTTTTAATAATTGTTACAATTTTCACAAATTTTAAAAATTTACTAAG
1 TAAATTTTACAATTTTTAATAATTGTTAAAATTTTCACAAATTTTAAAAATTTACTAAG
* * * * **
49555957 TAAA-TTTACAA-TTTTAATCATTTTTATAAATTTTTATATTTTTTAAAAATTT
1 TAAATTTTACAATTTTTAATAATTGTTA-AAATTTTCACAAATTTTAAAAATTT
49556009 CAATTTCTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
57 13 0.30
58 27 0.61
59 4 0.09
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (59 bp):
TAAATTTTACAATTTTTAATAATTGTTAAAATTTTCACAAATTTTAAAAATTTACTAAG
Found at i:49555990 original size:19 final size:18
Alignment explanation
Indices: 49555966--49556081 Score: 76
Period size: 18 Copynumber: 6.3 Consensus size: 18
49555956 GTAAATTTAC
49555966 AATTTTAATCATTTTTATA
1 AATTTTAAT-ATTTTTATA
*
49555985 AATTTTTATATTTTT-TAA
1 AATTTTAATATTTTTAT-A
* * *
49556003 AAATTTCA-ATTTCTAT-
1 AATTTTAATATTTTTATA
* *
49556019 AATTTTTACATTTTTATA
1 AATTTTAATATTTTTATA
* *
49556037 ATTTTACTAATTTTTTTATA
1 AATTT--TAATATTTTTATA
* *
49556057 ACTTTTAATAGTTTTAATA
1 AATTTTAATA-TTTTTATA
49556076 AATTTT
1 AATTTT
49556082 TTTCAAAAAC
Statistics
Matches: 75, Mismatches: 15, Indels: 14
0.72 0.14 0.13
Matches are distributed among these distances:
16 6 0.08
17 13 0.17
18 22 0.29
19 20 0.27
20 14 0.19
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.59
Consensus pattern (18 bp):
AATTTTAATATTTTTATA
Found at i:49555997 original size:18 final size:18
Alignment explanation
Indices: 49555966--49556082 Score: 71
Period size: 19 Copynumber: 6.4 Consensus size: 18
49555956 GTAAATTTAC
*
49555966 AATTTTAATCATTTTTATA
1 AATTTTTAT-ATTTTTATA
49555985 AATTTTTATATTTTT-TAA
1 AATTTTTATATTTTTAT-A
* * *
49556003 AAATTTCA-ATTTCTAT-
1 AATTTTTATATTTTTATA
*
49556019 AATTTTTACATTTTTAT-
1 AATTTTTATATTTTTATA
*
49556036 AATTTTACTAATTTTTTTATA
1 AATTTT--T-ATATTTTTATA
* * *
49556057 ACTTTTAATAGTTTTAATA
1 AATTTTTATA-TTTTTATA
49556076 AATTTTT
1 AATTTTT
49556083 TTCAAAAACT
Statistics
Matches: 75, Mismatches: 15, Indels: 16
0.71 0.14 0.15
Matches are distributed among these distances:
16 6 0.08
17 19 0.25
18 16 0.21
19 21 0.28
20 8 0.11
21 5 0.07
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (18 bp):
AATTTTTATATTTTTATA
Found at i:49556040 original size:9 final size:9
Alignment explanation
Indices: 49555961--49556051 Score: 55
Period size: 9 Copynumber: 10.3 Consensus size: 9
49555951 ACTAAGTAAA
*
49555961 TTTACAATT
1 TTTATAATT
* *
49555970 TTAATCATT
1 TTTATAATT
49555979 TTTATAAATT
1 TTTAT-AATT
*
49555989 TTTATATTT
1 TTTATAATT
**
49555998 TTTA-AAAA
1 TTTATAATT
*
49556006 TTT-CAATT
1 TTTATAATT
*
49556014 TCTATAATT
1 TTTATAATT
*
49556023 TTTA-CATT
1 TTTATAATT
49556031 TTTATAA-T
1 TTTATAATT
49556039 TTTACTAATT
1 TTTA-TAATT
49556049 TTT
1 TTT
49556052 TTATAACTTT
Statistics
Matches: 60, Mismatches: 16, Indels: 11
0.69 0.18 0.13
Matches are distributed among these distances:
8 20 0.33
9 28 0.47
10 12 0.20
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTATAATT
Found at i:49556050 original size:17 final size:17
Alignment explanation
Indices: 49556009--49556050 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
49555999 TTAAAAATTT
49556009 CAATTTCTATAATTTTTA
1 CAATTT-TATAATTTTTA
*
49556027 CATTTTTATAA-TTTTA
1 CAATTTTATAATTTTTA
49556043 CTAATTTT
1 C-AATTTT
49556051 TTTATAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 6 0.29
17 10 0.48
18 5 0.24
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.60
Consensus pattern (17 bp):
CAATTTTATAATTTTTA
Found at i:49556071 original size:20 final size:20
Alignment explanation
Indices: 49556029--49556071 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
49556019 AATTTTTACA
* *
49556029 TTTTTATAATTTTACTAATT
1 TTTTTATAATTTTAATAAGT
49556049 TTTTTATAACTTTTAAT-AGT
1 TTTTTATAA-TTTTAATAAGT
49556069 TTT
1 TTT
49556072 AATAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTTATAATTTTAATAAGT
Found at i:49556071 original size:21 final size:20
Alignment explanation
Indices: 49556029--49556071 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
49556019 AATTTTTACA
*
49556029 TTTTTATAATTTTACTAATT
1 TTTTTATAATTTTAATAATT
*
49556049 TTTTTATAACTTTTAATAGTT
1 TTTTTATAA-TTTTAATAATT
49556070 TT
1 TT
49556072 AATAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTTATAATTTTAATAATT
Found at i:49556130 original size:9 final size:9
Alignment explanation
Indices: 49556116--49556167 Score: 59
Period size: 9 Copynumber: 5.7 Consensus size: 9
49556106 CAATTTTTAC
49556116 AATTTTAAT
1 AATTTTAAT
* *
49556125 ATTTTTTAT
1 AATTTTAAT
49556134 AATTTTAAT
1 AATTTTAAT
* *
49556143 AAATTCTAAA
1 -AATTTTAAT
49556153 AATTTTAAT
1 AATTTTAAT
49556162 AATTTT
1 AATTTT
49556168 TTTTACAGAT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
9 27 0.79
10 7 0.21
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (9 bp):
AATTTTAAT
Found at i:49556130 original size:18 final size:18
Alignment explanation
Indices: 49556109--49556143 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
49556099 TTTTTTACAA
49556109 TTTTTACAATTTTAATAT
1 TTTTTACAATTTTAATAT
*
49556127 TTTTTATAATTTTAATA
1 TTTTTACAATTTTAATA
49556144 AATTCTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTTACAATTTTAATAT
Found at i:49557233 original size:18 final size:20
Alignment explanation
Indices: 49557198--49557234 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
49557188 AATTATTATA
49557198 AATTATTTAAAAATTGTAAC
1 AATTATTTAAAAATTGTAAC
49557218 AATTA-TTAAAAA-TGTAA
1 AATTATTTAAAAATTGTAA
49557235 AAACTTCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 7 0.41
20 5 0.29
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (20 bp):
AATTATTTAAAAATTGTAAC
Found at i:49557380 original size:26 final size:26
Alignment explanation
Indices: 49557323--49557380 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
49557313 CTTGTAAAAG
*
49557323 AATAAATTAAAAGTTGTAAAAATTAT
1 AATAAATTAAAAGTTGTAAAAATAAT
*
49557349 AATAAATATAAAATTTGTAAAAA-AAT
1 AATAAAT-TAAAAGTTGTAAAAATAAT
*
49557375 ATTAAA
1 AATAAA
49557381 AAGTTTAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 14 0.50
27 14 0.50
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (26 bp):
AATAAATTAAAAGTTGTAAAAATAAT
Found at i:49557418 original size:18 final size:18
Alignment explanation
Indices: 49557339--49557419 Score: 56
Period size: 18 Copynumber: 4.4 Consensus size: 18
49557329 TTAAAAGTTG
* * *
49557339 TAAAAATTATAATAAATA
1 TAAAAATTGTAAAAAAAA
*
49557357 TAAAATTTGTAAAAAAATA
1 TAAAAATTGTAAAAAAA-A
* **
49557376 TTAAAAAGTT-TAAGAAATT
1 -TAAAAA-TTGTAAAAAAAA
*
49557395 TGAAAATTGTAAAAAAAA
1 TAAAAATTGTAAAAAAAA
49557413 TAAAAAT
1 TAAAAAT
49557420 GTGAATATCG
Statistics
Matches: 46, Mismatches: 13, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
17 2 0.04
18 30 0.65
19 1 0.02
20 11 0.24
21 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
TAAAAATTGTAAAAAAAA
Found at i:49557471 original size:9 final size:9
Alignment explanation
Indices: 49557453--49557498 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
49557443 GAATTATTTT
49557453 AATTAGTAAA
1 AATTA-TAAA
49557463 AATTATAAA
1 AATTATAAA
* *
49557472 AATCATTAA
1 AATTATAAA
49557481 AATATATAAA
1 AAT-TATAAA
49557491 AATTATAA
1 AATTATAA
49557499 TGTTCTTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
9 19 0.61
10 12 0.39
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
AATTATAAA
Found at i:49558109 original size:33 final size:33
Alignment explanation
Indices: 49558072--49558138 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
49558062 GTACAATTTA
* *
49558072 CCAAAAATTAATGTTGTTAGGTAGG-AAATGGTC
1 CCAAAAAATAATGTTGATAGGT-GGTAAATGGTC
49558105 CCAAAAAATAATGTTGATAGGTGGTAAATGGTC
1 CCAAAAAATAATGTTGATAGGTGGTAAATGGTC
49558138 C
1 C
49558139 ACCCATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 2 0.06
33 29 0.94
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.28
Consensus pattern (33 bp):
CCAAAAAATAATGTTGATAGGTGGTAAATGGTC
Found at i:49563398 original size:29 final size:29
Alignment explanation
Indices: 49563359--49563414 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
49563349 AAAAAAATTT
*
49563359 GATCAAATTAATCCCTCTACTATTAAATG
1 GATCAAATTAATCCATCTACTATTAAATG
* * *
49563388 GATCAATTTAATCTATGTACTATTAAA
1 GATCAAATTAATCCATCTACTATTAAA
49563415 AAGAATCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (29 bp):
GATCAAATTAATCCATCTACTATTAAATG
Found at i:49565742 original size:19 final size:20
Alignment explanation
Indices: 49565714--49565755 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
49565704 ATATATAATG
**
49565714 ATTAAGAAAATATTAAAAAA
1 ATTAAGAAAATAGAAAAAAA
49565734 ATTAA-AAAATAGAAAAAAA
1 ATTAAGAAAATAGAAAAAAA
49565753 ATT
1 ATT
49565756 CAATTGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (20 bp):
ATTAAGAAAATAGAAAAAAA
Found at i:49565867 original size:20 final size:20
Alignment explanation
Indices: 49565819--49565871 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
49565809 CGGGTCAATT
* *
49565819 AATTTTAAATTTTTTTTAAA
1 AATTATAAATATTTTTTAAA
* *
49565839 TATCA-AAATATTTTTTAAA
1 AATTATAAATATTTTTTAAA
49565858 AATTATAAATATTT
1 AATTATAAATATTT
49565872 AAAAAATTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
AATTATAAATATTTTTTAAA
Found at i:49577430 original size:24 final size:24
Alignment explanation
Indices: 49577397--49577443 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
49577387 AAAAGAGAAT
49577397 GAAAAAT-AAAGAAGAATAAAAAAG
1 GAAAAATAAAAGAA-AATAAAAAAG
* *
49577421 GAAAATTAAAAGAACATAAAAAA
1 GAAAAATAAAAGAAAATAAAAAA
49577444 AATTAAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.74, C:0.02, G:0.13, T:0.11
Consensus pattern (24 bp):
GAAAAATAAAAGAAAATAAAAAAG
Found at i:49577952 original size:125 final size:126
Alignment explanation
Indices: 49577803--49578049 Score: 417
Period size: 126 Copynumber: 2.0 Consensus size: 126
49577793 GATAGATGTA
* *
49577803 ACATATAAATAGACCAAAAGTTAAAAAA-CATTTAATTTAG-TGCGATCAGCCCCTTTTTCAGCC
1 ACATATAAATAGACCAAAAGTTAAAAAAGCATTTAATTTAGTTG-AATCAACCCCTTTTTCAGCC
*
49577866 AATTTAAAAAGGATAATTGTTGCATCATATCCTTGAAAATTTGATCCTTCAATACTTTAGTC
65 AATTTAAAAAGGATAATTGTTGCATCATATCCTTGAAAATTTGATCCCTCAATACTTTAGTC
* *
49577928 ACATATAAATAGACCAAAAGTTAAAAAAGCATTTAATTTGGTTGAATCAACCCTTTTTTCAGCCA
1 ACATATAAATAGACCAAAAGTTAAAAAAGCATTTAATTTAGTTGAATCAACCCCTTTTTCAGCCA
*
49577993 ATTTAAAAAGGATAATTGTTGCATCATATCCTTGAACATTTGATCCCTCAATACTTT
66 ATTTAAAAAGGATAATTGTTGCATCATATCCTTGAAAATTTGATCCCTCAATACTTT
49578050 CGTCCTGTGC
Statistics
Matches: 114, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
125 28 0.25
126 84 0.74
127 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (126 bp):
ACATATAAATAGACCAAAAGTTAAAAAAGCATTTAATTTAGTTGAATCAACCCCTTTTTCAGCCA
ATTTAAAAAGGATAATTGTTGCATCATATCCTTGAAAATTTGATCCCTCAATACTTTAGTC
Found at i:49578505 original size:18 final size:17
Alignment explanation
Indices: 49578464--49578507 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
49578454 ATGCTTTTTG
49578464 AAAAATTATTTTTAAAA
1 AAAAATTATTTTTAAAA
**
49578481 AATAAATTATTTATTTTAA
1 AA-AAATTATTT-TTAAAA
49578500 AAAAATTA
1 AAAAATTA
49578508 ATATTTTCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 15 0.65
19 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAAATTATTTTTAAAA
Found at i:49578512 original size:21 final size:22
Alignment explanation
Indices: 49578469--49578513 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
49578459 TTTTGAAAAA
*
49578469 TTATTTTTAAAAAATAAATTAT
1 TTATTTTAAAAAAATAAATTAT
*
49578491 TTATTTTAAAAAAATTAA-TAT
1 TTATTTTAAAAAAATAAATTAT
49578512 TT
1 TT
49578514 TCTGATGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATTTTAAAAAAATAAATTAT
Found at i:49581329 original size:22 final size:22
Alignment explanation
Indices: 49581302--49581355 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 22
49581292 TTTGGATTAA
49581302 AATTAAATTGTAATTTTTATAAT
1 AATTAAATTGTAATTTTTA-AAT
*
49581325 -ATTAAAAATGTAATTTTTAAAT
1 AATT-AAATTGTAATTTTTAAAT
49581347 AATTAAATT
1 AATTAAATT
49581356 AAAATTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (22 bp):
AATTAAATTGTAATTTTTAAAT
Found at i:49581373 original size:30 final size:30
Alignment explanation
Indices: 49581337--49581395 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
49581327 TAAAAATGTA
*
49581337 ATTTTTAAATAATTAAATTAAAATTTTATC
1 ATTTTTAAATAATTAAAATAAAATTTTATC
* * *
49581367 ATTTTTAAGTGATTAAAATATAATTTTAT
1 ATTTTTAAATAATTAAAATAAAATTTTAT
49581396 TTATATTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (30 bp):
ATTTTTAAATAATTAAAATAAAATTTTATC
Found at i:49582310 original size:16 final size:17
Alignment explanation
Indices: 49582272--49582311 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
49582262 AATGCTTTTC
*
49582272 AAAAGTGTTTTTGAGTTA
1 AAAAGTATTTTTGAG-TA
49582290 AAAAGTATTTTTGAG-A
1 AAAAGTATTTTTGAGTA
49582306 AAAAGT
1 AAAAGT
49582312 TAAAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
18 14 0.67
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (17 bp):
AAAAGTATTTTTGAGTA
Found at i:49583422 original size:24 final size:24
Alignment explanation
Indices: 49583395--49583445 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
49583385 AGAAATAATC
*
49583395 TTTCAATTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTATTTAATTG
*
49583419 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTAATTG
49583443 TTT
1 TTT
49583446 GAGTCAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTAATTG
Found at i:49583454 original size:24 final size:24
Alignment explanation
Indices: 49583395--49583457 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
49583385 AGAAATAATC
* *
49583395 TTTCAATTAAACTCTGTTTAATTG
1 TTTCAATCAAACTCTATTTAATTG
* *
49583419 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATCAAACTCTATTTAATTG
* *
49583443 TTTGAGTCAAACTCT
1 TTTCAATCAAACTCT
49583458 TATTAGTCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (24 bp):
TTTCAATCAAACTCTATTTAATTG
Found at i:49585443 original size:24 final size:24
Alignment explanation
Indices: 49585392--49585446 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
49585382 TCTTTCTGTT
*
49585392 AAACTCTGTTTAATTGTTTCAATT
1 AAACTCTGTTTAATTGTTTCAATC
* * *
49585416 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTAATTGTTTCAATC
49585440 AAACTCT
1 AAACTCT
49585447 TATTAATCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (24 bp):
AAACTCTGTTTAATTGTTTCAATC
Done.